I would like to create a PC that is a permanently blinded witch (born without sight). In her early levels she will not have access to magical items or feats that grant other forms of vision. Would it be possible for her to guess where a foe is or otherwise determine where the target is for her Hexes?
Yes, but prepare to work your blind butt off
Just about everything in 3.Pf cares about line of effect, though PF's description only talks about spells. If you're firing an arrow, casting a spell, swinging a sword, or otherwise attempting to affect a creature you need to be able to define line of effect or have an ability that ignores it (for example, Astral Projection). Rather more importantly, since Line of Sight is a specific variant of Line of Effect it's...not 'lesser', but more case-based. An ability only requires LoS if it's specifically called out as needing it.
Being blind doesn't complicate Line of Effect one whit. However, it does make knowing that a creature or object is there to affect a lot more complicated. You can use the Perception skill to pinpoint the square an enemy is in, which should be enough for any Hex that doesn't require an attack roll (for the ones that do the enemy benefits from full concealment). If you've got Scent or can acquire it you won't need to do that, or your familiar can identify the square the enemy is in to you (sadly you cannot share its senses). Find a solution that works for you and run with it.